Put compute_snap back
This commit is contained in:
rohskopf
720
src/ML-SNAP/compute_snap.cpp
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720
src/ML-SNAP/compute_snap.cpp
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@ -0,0 +1,720 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_snap.h"
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#include "sna.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "force.h"
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#include "pair.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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enum{SCALAR,VECTOR,ARRAY};
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ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snap(nullptr),
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snapall(nullptr), snap_peratom(nullptr), radelem(nullptr), wjelem(nullptr),
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sinnerelem(nullptr), dinnerelem(nullptr), snaptr(nullptr)
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{
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array_flag = 1;
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extarray = 0;
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// begin code common to all SNAP computes
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double rfac0, rmin0;
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int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
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int ntypes = atom->ntypes;
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int nargmin = 6 + 2 * ntypes;
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if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
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// default values
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rmin0 = 0.0;
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switchflag = 1;
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bzeroflag = 1;
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quadraticflag = 0;
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bikflag = 0;
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dgradflag = 0;
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chemflag = 0;
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bnormflag = 0;
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wselfallflag = 0;
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switchinnerflag = 0;
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nelements = 1;
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// process required arguments
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memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types
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memory->create(wjelem, ntypes + 1, "sna/atom:wjelem");
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rcutfac = utils::numeric(FLERR, arg[3], false, lmp);
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rfac0 = utils::numeric(FLERR, arg[4], false, lmp);
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twojmax = utils::inumeric(FLERR, arg[5], false, lmp);
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for (int i = 0; i < ntypes; i++)
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radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp);
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for (int i = 0; i < ntypes; i++)
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wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp);
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// construct cutsq
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double cut;
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cutmax = 0.0;
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memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq");
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for (int i = 1; i <= ntypes; i++) {
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cut = 2.0 * radelem[i] * rcutfac;
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if (cut > cutmax) cutmax = cut;
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cutsq[i][i] = cut * cut;
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for (int j = i + 1; j <= ntypes; j++) {
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cut = (radelem[i] + radelem[j]) * rcutfac;
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cutsq[i][j] = cutsq[j][i] = cut * cut;
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}
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}
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// set local input checks
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int sinnerflag = 0;
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int dinnerflag = 0;
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// process optional args
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int iarg = nargmin;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "rmin0") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "switchflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "bzeroflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "quadraticflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "chem") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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chemflag = 1;
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memory->create(map, ntypes + 1, "compute_sna_grid:map");
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nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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for (int i = 0; i < ntypes; i++) {
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int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp);
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if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style);
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map[i + 1] = jelem;
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}
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iarg += 2 + ntypes;
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} else if (strcmp(arg[iarg], "bnormflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "wselfallflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "bikflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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bikflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg],"dgradflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snap command");
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dgradflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snap command");
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switchinnerflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg], "sinner") == 0) {
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iarg++;
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if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style);
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memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem");
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for (int i = 0; i < ntypes; i++)
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sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
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sinnerflag = 1;
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iarg += ntypes;
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} else if (strcmp(arg[iarg], "dinner") == 0) {
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iarg++;
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if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style);
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memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem");
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for (int i = 0; i < ntypes; i++)
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dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
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dinnerflag = 1;
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iarg += ntypes;
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} else
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error->all(FLERR, "Illegal compute {} command", style);
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}
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if (switchinnerflag && !(sinnerflag && dinnerflag))
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error->all(
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FLERR,
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"Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword",
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style);
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if (!switchinnerflag && (sinnerflag || dinnerflag))
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error->all(
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FLERR,
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"Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword",
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style);
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if (dgradflag && !bikflag)
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error->all(FLERR,"Illegal compute snap command: dgradflag=1 requires bikflag=1");
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if (dgradflag && quadraticflag)
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error->all(FLERR,"Illegal compute snap command: dgradflag=1 not implemented for quadratic SNAP");
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snaptr = new SNA(lmp, rfac0, twojmax,
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rmin0, switchflag, bzeroflag,
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chemflag, bnormflag, wselfallflag,
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nelements, switchinnerflag);
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ncoeff = snaptr->ncoeff;
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nvalues = ncoeff;
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if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2;
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// end code common to all SNAP computes
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ndims_force = 3;
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ndims_virial = 6;
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yoffset = nvalues;
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zoffset = 2 * nvalues;
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natoms = atom->natoms;
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bik_rows = 1;
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if (bikflag) bik_rows = natoms;
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dgrad_rows = ndims_force*natoms;
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size_array_rows = bik_rows+dgrad_rows + ndims_virial;
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if (dgradflag){
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size_array_rows = bik_rows + 3*natoms*natoms + 1;
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size_array_cols = nvalues + 3;
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error->warning(FLERR,"dgradflag=1 creates a N^2 array, beware of large systems.");
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}
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else size_array_cols = nvalues*atom->ntypes + 1;
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lastcol = size_array_cols-1;
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ndims_peratom = ndims_force;
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size_peratom = ndims_peratom*nvalues*atom->ntypes;
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nmax = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSnap::~ComputeSnap()
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{
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memory->destroy(snap);
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memory->destroy(snapall);
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memory->destroy(snap_peratom);
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memory->destroy(radelem);
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memory->destroy(wjelem);
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memory->destroy(cutsq);
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delete snaptr;
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if (chemflag) memory->destroy(map);
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if (switchinnerflag) {
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memory->destroy(sinnerelem);
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memory->destroy(dinnerelem);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSnap::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Compute snap requires a pair style be defined");
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if (cutmax > force->pair->cutforce){
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error->all(FLERR,"Compute snap cutoff is longer than pairwise cutoff");
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}
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// need an occasional full neighbor list
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neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
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if (modify->get_compute_by_style("snap").size() > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute snap");
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snaptr->init();
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// allocate memory for global array
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memory->create(snap,size_array_rows,size_array_cols,
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"snap:snap");
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memory->create(snapall,size_array_rows,size_array_cols,
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"snap:snapall");
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array = snapall;
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// find compute for reference energy
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std::string id_pe = std::string("thermo_pe");
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int ipe = modify->find_compute(id_pe);
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if (ipe == -1)
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error->all(FLERR,"compute thermo_pe does not exist.");
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c_pe = modify->compute[ipe];
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// add compute for reference virial tensor
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std::string id_virial = std::string("snap_press");
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std::string pcmd = id_virial + " all pressure NULL virial";
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modify->add_compute(pcmd);
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int ivirial = modify->find_compute(id_virial);
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if (ivirial == -1)
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error->all(FLERR,"compute snap_press does not exist.");
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c_virial = modify->compute[ivirial];
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSnap::compute_array()
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{
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int ntotal = atom->nlocal + atom->nghost;
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invoked_array = update->ntimestep;
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// grow snap_peratom array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(snap_peratom);
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nmax = atom->nmax;
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memory->create(snap_peratom,nmax,size_peratom,
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"snap:snap_peratom");
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}
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// clear global array
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for (int irow = 0; irow < size_array_rows; irow++){
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for (int icoeff = 0; icoeff < size_array_cols; icoeff++){
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snap[irow][icoeff] = 0.0;
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}
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}
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// clear local peratom array
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for (int i = 0; i < ntotal; i++)
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for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
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snap_peratom[i][icoeff] = 0.0;
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}
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// invoke full neighbor list (will copy or build if necessary)
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neighbor->build_one(list);
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const int inum = list->inum;
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const int* const ilist = list->ilist;
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const int* const numneigh = list->numneigh;
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int** const firstneigh = list->firstneigh;
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int * const type = atom->type;
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// compute sna derivatives for each atom in group
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// use full neighbor list to count atoms less than cutoff
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double** const x = atom->x;
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const int* const mask = atom->mask;
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int ninside;
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int numneigh_sum = 0;
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int dgrad_row_indx;
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for (int ii = 0; ii < inum; ii++) {
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int irow = 0;
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if (bikflag) irow = atom->tag[ilist[ii] & NEIGHMASK]-1;
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const int i = ilist[ii];
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if (mask[i] & groupbit) {
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const double xtmp = x[i][0];
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const double ytmp = x[i][1];
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const double ztmp = x[i][2];
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const int itype = type[i];
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int ielem = 0;
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if (chemflag)
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ielem = map[itype];
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const double radi = radelem[itype];
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const int* const jlist = firstneigh[i];
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const int jnum = numneigh[i];
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const int typeoffset_local = ndims_peratom*nvalues*(itype-1);
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const int typeoffset_global = nvalues*(itype-1);
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if (dgradflag){
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// dBi/dRi tags
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][0] = atom->tag[i]-1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][1] = atom->tag[i]-1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][2] = 0;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 1][0] = atom->tag[i]-1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 1][1] = atom->tag[i]-1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 1][2] = 1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][0] = atom->tag[i]-1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][1] = atom->tag[i]-1;
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snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][2] = 2;
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// dBi/dRj tags
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for (int j=0; j<natoms; j++){
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][0] = atom->tag[i]-1;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][1] = j;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 0][2] = 0;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 1][0] = atom->tag[i]-1;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 1][1] = j;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 1][2] = 1;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 2][0] = atom->tag[i]-1;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 2][1] = j;
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snap[bik_rows + ((j)*3*natoms) + 3*(atom->tag[i]-1) + 2][2] = 2;
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}
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}
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// insure rij, inside, and typej are of size jnum
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snaptr->grow_rij(jnum);
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// rij[][3] = displacements between atom I and those neighbors
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// inside = indices of neighbors of I within cutoff
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// typej = types of neighbors of I within cutoff
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// note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi
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// assign quantities in snaptr
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ninside=0;
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for (int jj = 0; jj < jnum; jj++) {
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int j = jlist[jj];
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j &= NEIGHMASK;
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|
||||
const double delx = x[j][0] - xtmp;
|
||||
const double dely = x[j][1] - ytmp;
|
||||
const double delz = x[j][2] - ztmp;
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
int jtype = type[j];
|
||||
int jelem = 0;
|
||||
if (chemflag)
|
||||
jelem = map[jtype];
|
||||
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
|
||||
snaptr->rij[ninside][0] = delx;
|
||||
snaptr->rij[ninside][1] = dely;
|
||||
snaptr->rij[ninside][2] = delz;
|
||||
snaptr->inside[ninside] = j;
|
||||
snaptr->wj[ninside] = wjelem[jtype];
|
||||
snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
|
||||
if (switchinnerflag) {
|
||||
snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]);
|
||||
snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]);
|
||||
}
|
||||
if (chemflag) snaptr->element[ninside] = jelem;
|
||||
ninside++;
|
||||
}
|
||||
}
|
||||
|
||||
// compute bispectrum for atom i
|
||||
|
||||
snaptr->compute_ui(ninside, ielem);
|
||||
snaptr->compute_zi();
|
||||
snaptr->compute_bi(ielem);
|
||||
|
||||
// loop over neighbors for descriptors derivatives
|
||||
|
||||
for (int jj = 0; jj < ninside; jj++) {
|
||||
const int j = snaptr->inside[jj];
|
||||
|
||||
snaptr->compute_duidrj(jj);
|
||||
snaptr->compute_dbidrj();
|
||||
|
||||
// accumulate dBi/dRi, -dBi/dRj
|
||||
|
||||
if (!dgradflag) {
|
||||
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
double *snadj = snap_peratom[j]+typeoffset_local;
|
||||
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
|
||||
snadi[icoeff] += snaptr->dblist[icoeff][0];
|
||||
snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
|
||||
snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
|
||||
|
||||
snadj[icoeff] -= snaptr->dblist[icoeff][0];
|
||||
snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
|
||||
snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
|
||||
}
|
||||
|
||||
if (quadraticflag) {
|
||||
const int quadraticoffset = ncoeff;
|
||||
snadi += quadraticoffset;
|
||||
snadj += quadraticoffset;
|
||||
int ncount = 0;
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
double bi = snaptr->blist[icoeff];
|
||||
double bix = snaptr->dblist[icoeff][0];
|
||||
double biy = snaptr->dblist[icoeff][1];
|
||||
double biz = snaptr->dblist[icoeff][2];
|
||||
|
||||
// diagonal elements of quadratic matrix
|
||||
|
||||
double dbxtmp = bi*bix;
|
||||
double dbytmp = bi*biy;
|
||||
double dbztmp = bi*biz;
|
||||
|
||||
snadi[ncount] += dbxtmp;
|
||||
snadi[ncount+yoffset] += dbytmp;
|
||||
snadi[ncount+zoffset] += dbztmp;
|
||||
snadj[ncount] -= dbxtmp;
|
||||
snadj[ncount+yoffset] -= dbytmp;
|
||||
snadj[ncount+zoffset] -= dbztmp;
|
||||
|
||||
ncount++;
|
||||
|
||||
// upper-triangular elements of quadratic matrix
|
||||
|
||||
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
|
||||
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
|
||||
+ bix*snaptr->blist[jcoeff];
|
||||
double dbytmp = bi*snaptr->dblist[jcoeff][1]
|
||||
+ biy*snaptr->blist[jcoeff];
|
||||
double dbztmp = bi*snaptr->dblist[jcoeff][2]
|
||||
+ biz*snaptr->blist[jcoeff];
|
||||
|
||||
snadi[ncount] += dbxtmp;
|
||||
snadi[ncount+yoffset] += dbytmp;
|
||||
snadi[ncount+zoffset] += dbztmp;
|
||||
snadj[ncount] -= dbxtmp;
|
||||
snadj[ncount+yoffset] -= dbytmp;
|
||||
snadj[ncount+zoffset] -= dbztmp;
|
||||
|
||||
ncount++;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
|
||||
// add to snap array for this proc
|
||||
|
||||
// dBi/dRj
|
||||
|
||||
snap[bik_rows + ((atom->tag[j]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][icoeff+3] -= snaptr->dblist[icoeff][0];
|
||||
snap[bik_rows + ((atom->tag[j]-1)*3*natoms) + 3*(atom->tag[i]-1) + 1][icoeff+3] -= snaptr->dblist[icoeff][1];
|
||||
snap[bik_rows + ((atom->tag[j]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][icoeff+3] -= snaptr->dblist[icoeff][2];
|
||||
|
||||
// dBi/dRi
|
||||
|
||||
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 0][icoeff+3] += snaptr->dblist[icoeff][0];
|
||||
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 1][icoeff+3] += snaptr->dblist[icoeff][1];
|
||||
snap[bik_rows + ((atom->tag[i]-1)*3*natoms) + 3*(atom->tag[i]-1) + 2][icoeff+3] += snaptr->dblist[icoeff][2];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
} // loop over jj inside
|
||||
|
||||
// accumulate Bi
|
||||
|
||||
if (!dgradflag) {
|
||||
|
||||
// linear contributions
|
||||
|
||||
int k = typeoffset_global;
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
|
||||
snap[irow][k++] += snaptr->blist[icoeff];
|
||||
|
||||
// quadratic contributions
|
||||
|
||||
if (quadraticflag) {
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
double bveci = snaptr->blist[icoeff];
|
||||
snap[irow][k++] += 0.5*bveci*bveci;
|
||||
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
|
||||
double bvecj = snaptr->blist[jcoeff];
|
||||
snap[irow][k++] += bveci*bvecj;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
int k = 3;
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
|
||||
snap[irow][k++] += snaptr->blist[icoeff];
|
||||
numneigh_sum += ninside;
|
||||
}
|
||||
|
||||
} // if (mask[i] & groupbit)
|
||||
|
||||
} // for (int ii = 0; ii < inum; ii++) {
|
||||
|
||||
// accumulate bispectrum force contributions to global array
|
||||
|
||||
if (!dgradflag) {
|
||||
|
||||
for (int itype = 0; itype < atom->ntypes; itype++) {
|
||||
const int typeoffset_local = ndims_peratom*nvalues*itype;
|
||||
const int typeoffset_global = nvalues*itype;
|
||||
for (int icoeff = 0; icoeff < nvalues; icoeff++) {
|
||||
for (int i = 0; i < ntotal; i++) {
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
int iglobal = atom->tag[i];
|
||||
int irow = 3*(iglobal-1)+bik_rows;
|
||||
snap[irow++][icoeff+typeoffset_global] += snadi[icoeff];
|
||||
snap[irow++][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
|
||||
snap[irow][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
// accumulate forces to global array
|
||||
|
||||
if (!dgradflag) {
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
int iglobal = atom->tag[i];
|
||||
int irow = 3*(iglobal-1)+bik_rows;
|
||||
snap[irow++][lastcol] = atom->f[i][0];
|
||||
snap[irow++][lastcol] = atom->f[i][1];
|
||||
snap[irow][lastcol] = atom->f[i][2];
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
// for dgradflag=1, put forces at first 3 columns of bik rows
|
||||
|
||||
for (int i=0; i<atom->nlocal; i++){
|
||||
int iglobal = atom->tag[i];
|
||||
snap[iglobal-1][0+0] = atom->f[i][0];
|
||||
snap[iglobal-1][0+1] = atom->f[i][1];
|
||||
snap[iglobal-1][0+2] = atom->f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
// accumulate bispectrum virial contributions to global array
|
||||
|
||||
dbdotr_compute();
|
||||
|
||||
// sum up over all processes
|
||||
|
||||
MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// assign energy to last column
|
||||
|
||||
if (!dgradflag) {
|
||||
for (int i = 0; i < bik_rows; i++) snapall[i][lastcol] = 0;
|
||||
int irow = 0;
|
||||
double reference_energy = c_pe->compute_scalar();
|
||||
snapall[irow][lastcol] = reference_energy;
|
||||
|
||||
} else {
|
||||
|
||||
// assign reference energy right after the dgrad rows, first column
|
||||
|
||||
int irow = bik_rows + 3*natoms*natoms;
|
||||
double reference_energy = c_pe->compute_scalar();
|
||||
snapall[irow][0] = reference_energy;
|
||||
}
|
||||
|
||||
// assign virial stress to last column
|
||||
// switch to Voigt notation
|
||||
|
||||
if (!dgradflag) {
|
||||
c_virial->compute_vector();
|
||||
int irow = 3*natoms+bik_rows;
|
||||
snapall[irow++][lastcol] = c_virial->vector[0];
|
||||
snapall[irow++][lastcol] = c_virial->vector[1];
|
||||
snapall[irow++][lastcol] = c_virial->vector[2];
|
||||
snapall[irow++][lastcol] = c_virial->vector[5];
|
||||
snapall[irow++][lastcol] = c_virial->vector[4];
|
||||
snapall[irow][lastcol] = c_virial->vector[3];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute global virial contributions via summing r_i.dB^j/dr_i over
|
||||
own & ghost atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeSnap::dbdotr_compute()
|
||||
{
|
||||
|
||||
// no virial terms for dgrad yet
|
||||
|
||||
if (dgradflag) return;
|
||||
|
||||
double **x = atom->x;
|
||||
|
||||
int irow0 = bik_rows+ndims_force*natoms;
|
||||
|
||||
// sum over bispectrum contributions to forces
|
||||
// on all particles including ghosts
|
||||
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
for (int i = 0; i < nall; i++)
|
||||
for (int itype = 0; itype < atom->ntypes; itype++) {
|
||||
const int typeoffset_local = ndims_peratom*nvalues*itype;
|
||||
const int typeoffset_global = nvalues*itype;
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
for (int icoeff = 0; icoeff < nvalues; icoeff++) {
|
||||
double dbdx = snadi[icoeff];
|
||||
double dbdy = snadi[icoeff+yoffset];
|
||||
double dbdz = snadi[icoeff+zoffset];
|
||||
int irow = irow0;
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
|
||||
snap[irow][icoeff+typeoffset_global] += dbdy*x[i][0];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeSnap::memory_usage()
|
||||
{
|
||||
|
||||
double bytes = (double)size_array_rows*size_array_cols *
|
||||
sizeof(double); // snap
|
||||
bytes += (double)size_array_rows*size_array_cols *
|
||||
sizeof(double); // snapall
|
||||
bytes += (double)nmax*size_peratom * sizeof(double); // snap_peratom
|
||||
bytes += snaptr->memory_usage(); // SNA object
|
||||
int n = atom->ntypes+1;
|
||||
bytes += (double)n*sizeof(int); // map
|
||||
|
||||
return bytes;
|
||||
}
|
||||
Reference in New Issue
Block a user